Desarrollo de una aplicación de computador para analizar parámetros estadísticos genético-poblacionales de microsatélites en poblaciones humanas

La información y los datos genéticos que emanan hoy de las investigaciones del genoma humano demandan el desarrollo de herramientas informáticas capaces de procesar la gran cantidad de información disponible. La mayor cantidad de datos genéticos es el resultado de equipos que realizan el análisis simultáneo de cientos o miles de polimorfismos o variaciones genéticas, de nuevas técnicas de laboratorio de mayor rendimiento que, en conjunto, ofrecen una mayor disponibilidad de información en un corto espacio de tiempo. Esta problemática conduce a la necesidad de desarrollar nuevas herramientas informáticas capaces de lidiar con este mayor volumen de datos genéticos. En el caso de la genética de poblaciones, a pesar de que existen herramientas informáticas que permiten procesar y facilitar el análisis de los datos, estas tienen limitaciones como la falta de conocimiento de los usuarios de algunos lenguajes de programación para alimentar la información y otras herramientas informáticas no realizan todas las estimaciones que se requieren y otros presentan limitaciones en cuanto al número de datos que pueden incorporar o manejar. En algunos casos hay redundancia al tener que usarse dos o más herramientas para poder procesar un conjunto de datos de información genética. El presente trabajo tiene por objetivo el desarrollo de una herramienta informática basada en aplicaciones de computador comunes, en este caso Microsoft Excel® y que resuelva todos los problemas y las limitaciones descritas antes. El desarrollo del conjunto de subprogramas que constituyen a Lustro; permiten superar lo anterior, presentar los resultados en un ambiente sencillo, conocido y fácil de operar, simplificando de esta forma el proceso de adaptación del usuario del programa, sin entrenamiento previo, obteniéndose en corto tiempo el procesamiento de la información genética de interés.

Identificación y caracterización de las mutaciones en el gen GAA en pacientes colombianos afectados por la enfermedad de Pompe

La Enfermedad de Pompe (EP) es un desorden metabólico caracterizado por la deficiencia de alfa-glucosidasa acida (GAA), una enzima que cataliza la hidrolisis de las uniones glucosidicas α-1.4 y α-1,6 de glucógeno. Esta deficiencia resulta en acumulación de glucógeno en todos los tejidos, especialmente en musculo esquelético. Los pacientes con EP muestran un gran espectro de fenotipos con respecto a la edad de inicio, progresión de la enfermedad, severidad y tasa de progresión a muerte. El curso clínico de la enfermedad es principalmente determinado por la naturaleza de las variaciones genéticas de GAA quellevan a diferentes grados de deficiencia enzimática. Hasta la fecha alrededor de 400 distintas variaciones en la secuencia de GAA han sido descritas, y en algunos casos la correlación genotipo-fenotipo no es claramente evidente. En este estudio se describe el primer análisis genético y clínico de pacientes colombianos con EP en 13 individuos afectados. La secuenciación directa del gen GAA, revelo ocho distintas mutaciones relacionadas con la etiología de EP incluyendo dos nuevas mutaciones missense c.1106T>C (p.Leu369Pro) y c.2236T >C (p. Trp746Arg). Estudios funcionales in vitro mostraron que los cambios estructurales conferidos por ambas mutaciones no inhiben la síntesis del precursor de GAA de 110 KD pero afectan el procesamiento y el transporte intra-celular de la proteína.

Lack of association between PCK1 polymorphisms and obesity, physical activity, and fitness in European Youth Heart Study (EYHS)

Phosphoenolpyruvate carboxykinase-1 (PCK1) is the rate-limiting enzyme in the hepatic gluconeogenic pathway. Studies have shown that overexpression of Pck1 in mice results in obesity-related traits and higher levels of physical activity (PA). Therefore, our aims were to investigate whether common genetic variation in the PCK1 gene influences obesity-related traits, PA, and fitness, and to examine whether PA and fitness attenuate the influence of the PCK1 polymorphisms on obesity in children. Analyses were undertaken on data from Danish and Estonian children (958 boys and 1,104 girls) from the European Youth Heart Study (EYHS), a school-based, cross-sectional study of children (mean ± s.d. age: 9.6 ± 0.4 years) and adolescents (15.5 ± 0.5 years). We genotyped eight polymorphisms that captured the common genetic variations in the PCK1 gene. The association between the PCK1 polymorphisms and BMI, waist circumference (WC), sum of four skinfolds, PA, and fitness was tested using an additive model adjusted for age, age-group, gender, maturity, and country. Interactions were tested by including interaction terms in the model. None of the polymorphisms were significantly associated with BMI, WC, sum of four skinfolds, PA, and fitness, and also with the risk of being overweight or obese (P > 0.05). The interactions between the polymorphisms and age-group, gender, PA, and fitness were not statistically significant. This is the first study to comprehensively examine the association of PCK1 polymorphisms with obesity, PA, and fitness. Despite strong evidence from animal studies, our study in the EYHS cohort failed to identify an association of PCK1 polymorphisms with obesity, PA, and fitness.

Sexually Dimorphic Effect of the Val66Met Polymorphism of BDNF on Susceptibility to Alzheimer`s Disease: New Data and Meta-Analysis

Conflicting results have been reported as to whether genetic variations (Val66Met and C270T) of the brain-derived neurotrophic factor gene (RDNF) confer susceptibility to Alzheimer`s disease (AD). We genotyped these polymorphisms in a Japanese sample of 657 patients with AD and 525 controls, and obtained weak evidence of association for Val66Met (P = 0.063), but not for C270T. After stratification by sex, we found a significant allelic association between Val66Met and AD in women (P = 0.017), but not in men. To confirm these observations, we collected genotyping data for each sex from 16 research centers worldwide (4,711 patients and 4,537 controls in total). The meta-analysis revealed that there was a clear sex difference in the allelic association; the Met66 allele confers susceptibility to AD in women (odds ratio = 1.14, 95% CI 1.05-1.24, P = 0.002), but not in men. Our results provide evidence that the Met66 allele of BDNF has a sexually dimorphic effect on susceptibility to AD. (C) 2009 Wiley-Liss, Inc.

PCR primed with minisatellite core sequences yields species-specific patterns and assessment of population variability in fishes of the genus Brycon

Minisatellite core sequences were used as single primers in polymerase chain reaction (PCR) to amplify genomic DNA in a way similar to the random amplified polymorphic DNA methodology. This technique, known as Directed Amplification of Minisatellite-region DNA, was applied in order to differentiate three neotropical fish species (Brycon orbignyanus, B. microlepis and B. lundii ) and to detect possible genetic variations among samples of the threatened species, B. lundii , collected in two regions with distinct environmental conditions in the area of influence of a hydroelectric dam. Most primers generated species-specific banding patterns and high levels of intraspecific polymorphism. The genetic variation observed between the two sampling regions of B. lundii was also high enough to suggest the presence of distinct stocks of this species along the same river basin. The results demonstrated that minisatellite core sequences are potentially useful as single primers in PCR to assist in species and population identification. The observed genetic stock differentiation in B. lundii associated with ecological and demographic data constitute a crucial task to develop efficient conservation strategies in order to preserve the genetic diversity of this endangered fish species.

Differentiation of Acidithiobacillus ferrooxidans and A-thiooxidans strains based on 16S-23S rDNA spacer polymorphism analysis

Restriction fragment length polymorphism (RFLP) and sequence analyses of the PCR-amplified 16S-23S rDNA intergenic spacer (ITS) were used for differentiating Acidithiobacillus thiooxidans strains from other related acidithiobacilli, including A. ferrooxidans and A. caldus. RFLP fingerprints obtained with AluI, DdeI, HaeIII, HinfI and MspI enabled the differentiation of all Acidithiobacillus reference strains into species groups. The A. thiooxidans strains investigated (metal mine isolates) yielded identical RFLP patterns to the A. thiooxidans type strain (ATCC 19377(T)), except for strain DAMS, which had a distinct pattern for all enzymes tested. Fourteen A. ferrooxidans mine strains were assigned to 3 RFLP groups, the majority of which were grouped with A. ferrooxidans ATCC 23270(T). The spacer region of one representative strain from each of the RFLP groups obtained was subjected to sequence analysis, in addition to eleven additional A. thiooxidans strains isolated from sediment and water samples, and A. caldus DSM 8584(T). The tRNA(IIe) and tRNA(Ala) genes, present in all strains analyzed, showed high sequence similarity. Phylogenetic analysis of the ITS sequences differentiated all three Acidithiobacillus species. Inter- and infraspecific genetic variations detected were mainly due to the size and sequence polymorphism of the ITS3 region. Mantel tests showed no significant correlation between ITS sequence similarity and the geographical origin of strains. The results showed that the 16S-23S rDNA spacer region is a useful target for the development of molecular-based methods aimed at the detection, rapid differentiation and identification of acidithiobacilli. (C) 2004 Elsevier SAS. All rights reserved.

Parâmetros genéticos para caracteres de crescimento, de produção e tecnológicos da madeira em clones de Eucalyptus spp

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Estimativas de parâmetros genéticos para caracteres quantitativos em progênies de polinização aberta de Eucalyptus urophylla

Eucalyptus urophylla S. T. Blake is outstanding for valuable wood production potential, adaptation plasticity for different environmental conditions, and for tolerance to canker. However, genetic improvement of this specie in Brazil depends on the existence of genetic variability in the introduced populations. The objective of this study was to investigate the genetic variation and gains in quantitative traits in a population established in 1992 in Selvíria - MS. The progeny trial was established in a partially balanced, 8 x 8 lattice design, with 64 families, collected at Anhembi Experimental Station (IPEF/ESALQ/USP). Each plot was made up of eight trees planted in a 3 × 3 m spacing. Significant among families genetic variations were observed in diameter at breast height (DBH), bark type, stem form, and survival. Estimates of average family heritability were high for all traits, ranging from 0.50 to 0.85. The simulated selection by using multi-effect index showed that under a varying number of plants per family. This method is the most indicated to maximize genetic gains (7.24%) and the effective population size (69.3). These results are a useful support for the transformation of this test into a seedling seed orchard and to become a source of vegetative material to build a clonal seed orchard.

Outbreak of fungemia caused by Candida parapsilosis in a neonatal intensive care unit: Molecular investigation through microsatellite analysis

Background: Opportunistic infections are an increasingly common problem in hospitals, and the yeast Candida parapsilosis has emerged as an important nosocomial pathogen, especially in neonatal intensive care units (NICUs) where it has been responsible for outbreak cases. Risk factors for C. parapsilosis infection in neonates include prematurity, very low birth weight, prolonged hospitalization, indwelling central venous catheters, hyperalimentation, intravenous fatty emulsions and broad spectrum antibiotic therapy. Molecular methods are widely used to elucidate these hospital outbreaks, establishing genetic variations among strains of yeast. Aims: The aim of this study was to detect an outbreak of C. parapsilosis in an NICU at the Hospital das Clinicas , Faculty of Medicine of Botucatu, a tertiary hospital located in São Paulo, Brazil, using the molecular genotyping by the microsatellite markers analysis. Methods: A total of 11 cases of fungemia caused by C. parapsilosis were identified during a period of 43 days in the NICU. To confirm the outbreak all strains were molecularly typed using the technique of microsatellites. Results: Out of the 11 yeast samples studied, nine showed the same genotypic profile using the technique of microsatellites. Conclusions: Our study shows that the technique of microsatellites can be useful for these purposes. In conclusion, we detected the presence of an outbreak of C. parapsilosis in the NICU of the hospital analyzed, emphasizing the importance of using molecular tools, for the early detection of hospital outbreaks, and for the introduction of effective preventive measures, especially in NICUs. © 2012 Revista Iberoamericana de Micología.

Rastreamento de polimorfsmos no gene HIOMT e associações com os fenótipos circadianos

HIOMT is a gene that encodes hydroxyindole-O-methyltransfe-rase, the final enzyme in the melatonin synthesis pathway. As the timing of melatonin synthesis is different for morning and evening people, it is possible that polymorphisms in genes coding for the enzymes which participate in melatonin synthesis can influence this hormone synthesis and release patterns that may result in different circadian outputs. The aim of this study was to search for polymorphisms in the HIOMT gene and to verify possible associations between genetic variations in this gene and circadian phenotypes in a Brazilian population sample. Among the 44 extreme morning and the 48 extreme evening people, ten polymorphisms were found, being two of them not described so far. Haploview analyses showed linkage disequilibrium between pairs of polymorphisms in the promoter B region. Also, the haplotype AG (rs4446909, rs5989681) is associated with evening preference. The analysis of these data indicates that polymorphisms in the HIOMT gene exhibit a possible trend to influence circadian phenotypes in this Brazilian population sample, possibly affecting the rate and/or level of melatonin synthesis.

Determinantes genéticos, bioquímicos e clínicos na resposta ao uso de hidroxiureia na doença falciforme

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Phyllosticta citricarpa: diversidade genética temporal em pomares de citrus sinensis e sensibilidade a fungicidas

Pós-graduação em Agronomia (Genética e Melhoramento de Plantas) - FCAV

Análise da Frequência de Polimorfismos nos genes IL28B e IL28R1 em pacientes acometidos por Meningioma

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Estudo das alterações genéticas da Interleucina 28B em Astrocitomas

Pós-graduação em Pesquisa e Desenvolvimento (Biotecnologia Médica) - FMB

Vitamin D receptor polymorphisms in hypertensive disorders of pregnancy

Hypertension is the most common medical disorder in pregnancy, and a leading cause of maternal and neonatal morbidity and mortality. Vitamin D endocrine system has important influence on immune modulation and endothelial function, which play a role in preeclampsia (PE) and gestational hypertension (GH). Vitamin D receptor (VDR) is present in a large variety of cell types, including placental cells. We examined whether there is an association between VDR polymorphisms (FokI, ApaI and BsmI) with PE or with GH. Restriction fragment length polymorphism techniques were used to genotype 529 pregnant (154 with GH, 162 with PE, and 213 healthy pregnant-HP). VDR haplotype frequencies were inferred using the PHASE 2.1 program. We found similar genotype distributions for the three VDR polymorphisms in both PE and GH groups compared with the HP group (all P > 0.05). In parallel with these findings, the VDR haplotype frequency distribution was similar in both PE and GH groups compared with the HP group (all P > 0.05). Our results showing no significant association between VDR polymorphisms or haplotypes with PE or GH suggest that genetic variations in VDR do not predispose to hypertensive disorders of pregnancy.